Incidental Mutation 'R5202:Mbd4'
ID 400882
Institutional Source Beutler Lab
Gene Symbol Mbd4
Ensembl Gene ENSMUSG00000030322
Gene Name methyl-CpG binding domain protein 4
Synonyms Med1
MMRRC Submission 042777-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.192) question?
Stock # R5202 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 115817658-115830332 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 115826363 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 188 (D188E)
Ref Sequence ENSEMBL: ENSMUSP00000125619 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032469] [ENSMUST00000038234] [ENSMUST00000112923] [ENSMUST00000112925] [ENSMUST00000122816] [ENSMUST00000147282] [ENSMUST00000203643] [ENSMUST00000141305]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000032469
AA Change: D209E

PolyPhen 2 Score 0.427 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000032469
Gene: ENSMUSG00000030322
AA Change: D209E

DomainStartEndE-ValueType
MBD 66 142 1.25e-29 SMART
low complexity region 178 196 N/A INTRINSIC
PDB:1NGN|A 400 554 1e-111 PDB
SCOP:d1keaa_ 405 545 1e-23 SMART
Blast:ENDO3c 439 514 2e-6 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000038234
SMART Domains Protein: ENSMUSP00000045468
Gene: ENSMUSG00000030323

DomainStartEndE-ValueType
WD40 1 39 7.1e1 SMART
WD40 42 81 7.16e-10 SMART
WD40 83 120 1.54e0 SMART
WD40 122 160 1.43e0 SMART
WD40 162 208 2.29e1 SMART
WD40 210 249 1.91e1 SMART
WD40 251 290 3.45e-3 SMART
WD40 448 483 1.43e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112923
SMART Domains Protein: ENSMUSP00000108545
Gene: ENSMUSG00000030323

DomainStartEndE-ValueType
WD40 1 39 7.1e1 SMART
WD40 42 81 7.16e-10 SMART
WD40 83 120 1.54e0 SMART
WD40 122 160 1.43e0 SMART
Blast:WD40 163 267 3e-46 BLAST
WD40 269 308 1.91e1 SMART
WD40 310 349 3.45e-3 SMART
WD40 507 542 1.43e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112925
SMART Domains Protein: ENSMUSP00000108547
Gene: ENSMUSG00000030323

DomainStartEndE-ValueType
WD40 1 39 7.1e1 SMART
WD40 42 81 7.16e-10 SMART
WD40 83 120 1.54e0 SMART
WD40 122 160 1.43e0 SMART
WD40 162 208 2.29e1 SMART
WD40 210 249 1.91e1 SMART
WD40 251 290 3.45e-3 SMART
WD40 448 483 1.43e1 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000122816
AA Change: D209E

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000145433
Gene: ENSMUSG00000030322
AA Change: D209E

DomainStartEndE-ValueType
MBD 66 142 7.6e-32 SMART
low complexity region 178 196 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125889
Predicted Effect probably damaging
Transcript: ENSMUST00000147282
AA Change: D188E

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000125619
Gene: ENSMUSG00000030322
AA Change: D188E

DomainStartEndE-ValueType
MBD 45 121 1.25e-29 SMART
low complexity region 157 175 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000203643
SMART Domains Protein: ENSMUSP00000144930
Gene: ENSMUSG00000030322

DomainStartEndE-ValueType
Pfam:HhH-GPD 56 168 2.7e-5 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000203243
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133830
Predicted Effect probably benign
Transcript: ENSMUST00000141305
SMART Domains Protein: ENSMUSP00000138535
Gene: ENSMUSG00000030323

DomainStartEndE-ValueType
WD40 1 39 7.1e1 SMART
WD40 42 81 7.16e-10 SMART
WD40 83 120 1.54e0 SMART
low complexity region 124 134 N/A INTRINSIC
low complexity region 162 176 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcription from methylated gene promoters. This protein contains an MBD domain at the N-terminus that functions both in binding to methylated DNA and in protein interactions and a C-terminal mismatch-specific glycosylase domain that is involved in DNA repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]
PHENOTYPE: Mice homozygous for a null allele have an increased rate of DNA mutation, specifically at CpGs. [provided by MGI curators]
Allele List at MGI

All alleles(8) : Targeted(6) Gene trapped(2)

Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4932414N04Rik A T 2: 68,562,308 (GRCm39) M312L probably benign Het
Adam7 C A 14: 68,745,305 (GRCm39) D640Y possibly damaging Het
Alcam T C 16: 52,094,599 (GRCm39) Y384C probably damaging Het
Apob A G 12: 8,063,737 (GRCm39) E289G probably damaging Het
Arhgap15 A T 2: 43,953,869 (GRCm39) R198S probably benign Het
Bbs2 G T 8: 94,819,042 (GRCm39) S109* probably null Het
Bfsp1 T C 2: 143,668,891 (GRCm39) S569G probably benign Het
Chst9 A T 18: 15,586,296 (GRCm39) I89N probably benign Het
Cntln A C 4: 84,889,466 (GRCm39) E316D probably benign Het
Csde1 T G 3: 102,947,250 (GRCm39) D67E probably damaging Het
Csf2rb T G 15: 78,233,257 (GRCm39) S855A possibly damaging Het
Cyp4a10 T A 4: 115,389,812 (GRCm39) D472E probably damaging Het
Cyp4f18 C A 8: 72,762,940 (GRCm39) R49L probably benign Het
Daam1 G T 12: 71,991,048 (GRCm39) V221L unknown Het
Dbr1 T G 9: 99,465,944 (GRCm39) D507E probably benign Het
Dhrs7c A G 11: 67,706,627 (GRCm39) M188V probably benign Het
Dicer1 A T 12: 104,660,990 (GRCm39) L1688* probably null Het
Dmpk C G 7: 18,821,944 (GRCm39) L301V probably benign Het
E2f3 G A 13: 30,102,619 (GRCm39) T91I probably damaging Het
Etaa1 A T 11: 17,897,853 (GRCm39) V157E probably damaging Het
Foxp2 A T 6: 15,394,770 (GRCm39) T157S probably benign Het
Frem2 A G 3: 53,458,767 (GRCm39) V2034A probably benign Het
Fzd10 T C 5: 128,679,180 (GRCm39) V300A possibly damaging Het
Gbf1 A T 19: 46,256,893 (GRCm39) M778L probably benign Het
Gm17472 T A 6: 42,958,068 (GRCm39) N112K probably benign Het
Gria4 T C 9: 4,424,330 (GRCm39) K845R probably benign Het
Hspa4l T A 3: 40,736,001 (GRCm39) S541T probably benign Het
Igkv4-68 G A 6: 69,281,926 (GRCm39) R82C probably damaging Het
Itgb1 A T 8: 129,446,491 (GRCm39) I383F probably damaging Het
Kcnk12 T A 17: 88,054,033 (GRCm39) K210* probably null Het
Limch1 C G 5: 67,150,516 (GRCm39) D163E probably damaging Het
Myh9 C T 15: 77,665,310 (GRCm39) probably null Het
Nbeal2 T C 9: 110,473,734 (GRCm39) E28G probably damaging Het
Nfatc4 A G 14: 56,064,116 (GRCm39) E201G probably damaging Het
Nrap G A 19: 56,323,583 (GRCm39) H1330Y probably damaging Het
Nudt14 A G 12: 112,898,648 (GRCm39) S151P probably damaging Het
Or14c45 C A 7: 86,176,324 (GRCm39) R120S probably damaging Het
Or2ag2 T A 7: 106,485,803 (GRCm39) T74S possibly damaging Het
Or7e165 T A 9: 19,694,514 (GRCm39) F28L possibly damaging Het
Otx1 C A 11: 21,947,037 (GRCm39) A91S probably damaging Het
Paqr9 A G 9: 95,442,163 (GRCm39) D51G probably damaging Het
Pcgf5 T A 19: 36,414,583 (GRCm39) F80I probably damaging Het
Pkhd1 T G 1: 20,617,565 (GRCm39) S1007R probably benign Het
Rab30 T C 7: 92,485,121 (GRCm39) Y196H probably benign Het
Setd2 A T 9: 110,380,298 (GRCm39) D1371V probably damaging Het
Slc48a1 A T 15: 97,688,581 (GRCm39) I140F possibly damaging Het
Sorl1 A G 9: 41,944,879 (GRCm39) V882A probably benign Het
Sptbn2 G T 19: 4,774,212 (GRCm39) G88W probably damaging Het
Tdrd12 A G 7: 35,189,455 (GRCm39) V427A possibly damaging Het
Tekt2 T C 4: 126,218,463 (GRCm39) D69G probably benign Het
Tie1 C T 4: 118,337,707 (GRCm39) V463I probably benign Het
Tmem150c G T 5: 100,227,813 (GRCm39) H217N probably damaging Het
Tnks2 G A 19: 36,866,252 (GRCm39) G1080R probably damaging Het
Ttll4 G A 1: 74,727,011 (GRCm39) probably null Het
Other mutations in Mbd4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01516:Mbd4 APN 6 115,826,491 (GRCm39) missense probably damaging 0.99
IGL01545:Mbd4 APN 6 115,827,758 (GRCm39) missense probably damaging 1.00
IGL01657:Mbd4 APN 6 115,826,598 (GRCm39) missense probably damaging 0.99
IGL02406:Mbd4 APN 6 115,825,986 (GRCm39) missense possibly damaging 0.96
E0370:Mbd4 UTSW 6 115,826,116 (GRCm39) missense possibly damaging 0.91
R0025:Mbd4 UTSW 6 115,821,529 (GRCm39) critical splice donor site probably null
R0025:Mbd4 UTSW 6 115,821,529 (GRCm39) critical splice donor site probably null
R0538:Mbd4 UTSW 6 115,826,443 (GRCm39) missense probably damaging 0.99
R2085:Mbd4 UTSW 6 115,825,918 (GRCm39) missense probably benign 0.01
R4405:Mbd4 UTSW 6 115,826,076 (GRCm39) missense possibly damaging 0.92
R4464:Mbd4 UTSW 6 115,826,463 (GRCm39) missense probably damaging 0.99
R4780:Mbd4 UTSW 6 115,826,345 (GRCm39) missense probably benign
R4782:Mbd4 UTSW 6 115,822,283 (GRCm39) missense possibly damaging 0.49
R4799:Mbd4 UTSW 6 115,822,283 (GRCm39) missense probably benign 0.26
R4814:Mbd4 UTSW 6 115,826,260 (GRCm39) missense possibly damaging 0.85
R4860:Mbd4 UTSW 6 115,825,887 (GRCm39) missense possibly damaging 0.51
R4860:Mbd4 UTSW 6 115,825,887 (GRCm39) missense possibly damaging 0.51
R4976:Mbd4 UTSW 6 115,827,685 (GRCm39) missense possibly damaging 0.95
R5126:Mbd4 UTSW 6 115,825,929 (GRCm39) splice site probably null
R5485:Mbd4 UTSW 6 115,827,679 (GRCm39) missense probably benign 0.21
R6179:Mbd4 UTSW 6 115,822,386 (GRCm39) missense probably benign 0.00
R6661:Mbd4 UTSW 6 115,826,116 (GRCm39) nonsense probably null
R7008:Mbd4 UTSW 6 115,827,685 (GRCm39) missense possibly damaging 0.95
R7244:Mbd4 UTSW 6 115,821,564 (GRCm39) missense probably benign 0.00
R7723:Mbd4 UTSW 6 115,822,324 (GRCm39) missense possibly damaging 0.47
R7755:Mbd4 UTSW 6 115,821,546 (GRCm39) missense probably damaging 0.99
R7837:Mbd4 UTSW 6 115,826,500 (GRCm39) missense probably benign 0.20
R8032:Mbd4 UTSW 6 115,821,594 (GRCm39) missense probably damaging 1.00
R9707:Mbd4 UTSW 6 115,826,559 (GRCm39) missense probably benign 0.04
Predicted Primers PCR Primer
(F):5'- AACAGTCTCCCTTGCACAG -3'
(R):5'- TGCAGCCAAATGAAACTGAC -3'

Sequencing Primer
(F):5'- GACTTTCCTGTGGCACCAG -3'
(R):5'- TGACGTTTCAAAGCAGAACCTC -3'
Posted On 2016-07-06